Stemming from Shadow
by Reglee
Summary: ROOT is known for its loyal shinobi, but what would happen if one defected and became a part of Konoha's regular military? What if he became Naruto's friend? AU and OC. No pairings yet.


Disclaimer: I don't own Naruto.

Stemming from Shadow

Chapter 1:

The boy crept through the hallways of the ROOT base. For once, it was deserted, and he didn't need to worry about being watched. Some of the other trainees were mingling around, but he didn't need to worry about them. The important thing was that all of the sensei were absent. This hadn't happened for as long as he could remember.

He kept his breathing steady and went back to his room to gather his things. This was the opportunity he had been waiting for. Ever since he saw his sempai have to kill his partner, he had doubted ROOTs program. It seemed too inefficient to cull half of the trainees to finish the emotional training. There had to be another way. He would be dreading having to go through it himself, but she had died on a mission a few months ago.

He sealed away his tanto and mission pack, then grabbed his civilian clothes. He didn't put them on yet though, they would only draw suspicion inside the base. He walked toward one of the bases exits, which just happened to be in the same direction as the laundry room. None of the others even batted an eye at him.

He ducked inside a hallway. There were still guards posted at the entrance, it wouldn't matter though. He threw the dark blue jacket and black pants over his black training clothes and silently approached the entrance. His hands flashed through seals and he cast a genjutsu so they wouldn't even notice him. She was always better at combat and ninjutsu, while he was better at supporting her. It worked out for him here. He walked right past the older ROOT members and into the alleyway. His reflection stared back at him from a puddle. His short black hair and black eyes would help him blend in, but he hoped his pale skin wouldn't be a problem. He easily merged with the walking civilians in the street, just like doing an infiltration mission. He kept going for three blocks and entered a park.

It was midafternoon and there were still kids playing, both older and younger than him. He went and sat idly on a swing next to an older blonde boy so he plan out his next move. He didn't have a plan beyond getting out of the base. It had always seemed like a long shot anyway, but he knew that he still wasn't free. It wouldn't be hard to get caught by a ROOT member and get sent back. He just hoped that it took a while for them to notice he was gone. Theoretically, no one would notice his absence until there was a mission for him. He didn't think that they would expect him to stay in Konoha either.

He stayed on the swing and watched as more and more children left as it got darker. He still didn't know what to do, any plan he thought up was shot down just as fast. Something tapped his shoulder and he jerked upright. The blonde boy was standing next to him.

"Oi, didn't you hear me?" he shouted, crossing his arms. His blue eyes were looking at me expectantly, and he had whisker birthmarks on his cheeks.

"Sorry, what did you say?" His voice came out much quieter than the spiky-blonde haired kid's. He didn't want to attract any attention to himself.

"I said, I'm Naruto Uzumaki, and I'm going to be Hokage one day. Do you want to play ninja or something dattebayo?" He grinned at me, waiting for my answer. It would look bad if I turned him down and he caused a scene, and playing in the park would help him look like one of the other kids. No ROOT agent would look twice at a boy playing ninja in the park, this could work out for him.

"Yes, I would like to play a game," he said.

"Awesome!" Naruto yelled out. "What's your name?"

He hesitated, he couldn't give Naruto his callsign. He quickly thought of his last infiltration mission and used the name he was given then.

"I am Shin."

"Nice to meet ya Shin-kun! Now go hide, I'll come looking for you in a minute!"

He left the boy at the swings and silently climbed up the nearby tree. When the time was up, Naruto ran all around the park looking for him, but never once looked up. After about ten minutes of searching, he stopped near the tree and shouted for him to come out.

Shin dropped down next to Naruto, startling the boy.

"Gah, you were in the tree the whole time?" he shouted and groaned. "I never even thought to look there. Alright, it's your turn now."

They continued to play ninja as night fell. Naruto was surprisingly hard to find, even for a trained ninja like himself. They switched off multiple times, and he thought Naruto was gradually getting better at finding him. He had to start making small mistakes for that to happen though.

When the moon was high overhead, Naruto stopped the game. "Hey Shin-kun, don't you have anywhere to be? It's getting pretty late."

"No, Naruto-san. I have nowhere to stay so no one is expecting me anywhere."

"Well then you are coming home with me dattebayo! I can't let my new friend sleep in the streets!" Then he grabbed my arm and led me through the streets. Eventually, we approached an old apartment complex and we went to the top of it. It didn't look like many people lived there. Shin had no qualms going with Naruto. He had kept a lookout as they moved through the streets, and he didn't notice any ROOT agents following them. It would be safe to stay here.

Naruto opened his door and pushed Shin in. Naruto's apartment was decorated ninja posters and training equipment was scattered all over the floor. Dirty dishes piled in the sink. Shin frowned at the disorganized equipment, but didn't bring it up.

"Thank you for your hospitality Naruto-san."

"Hai hai, its nothing Shin-kun. And quit it with that san stuff."

He ended up sleeping on the couch after Naruto brought him some blankets. This was a good temporary solution, but he needed to figure out what he was going to do soon.

The next day they didn't do anything all morning. Naruto tried to ask him more about his life, but Shin just gave vague answers in return. All he gave up was that he was also an orphan. Naruto was surprised that he didn't recognize him, because he still recognized a lot of the other orphans from his time there. He just played it off the two year age difference and not playing in the same groups. Thankfully, Naruto took it all in stride and believed his excuses.

We ended up leaving the apartment to go out and eat. Surprisingly, Naruto didn't have a lot of food for someone that lived by himself. Shin kept his eyes open as they walked through the town. He didn't notice any ROOT agents, but he stayed on guard. He noticed a lot of people giving them glares too. (). They ended up at a ramen stand that Naruto seemed familiar with.

"Hey Ayame-neechan, get me usual dattebayo!"

"Hai, coming right up Naruto-kun. And who's your cute little friend?"

"Oh yeah this is Shin-kun! We met yesterday at the park and he's staying with me now!" Naruto said, mouth watering at the smell of ramen. "He's pretty cool, doesn't talk a lot though."

Shin bowed his head in greeting. "Hello Ayame-san, I'll take a chicken ramen please."

"Hai, good choice Shin-kun," she said with a smile. He didn't understand why she seemed happy about it though, it was just an order. He didn't understand why Naruto was so excited either.

An old man walked into the stand and sat down next to Naruto and Shin's eyes widened. That's the Hokage, what the heck is he doing in a ramen stand?

"Good morning Naruto-kun," he greeted warmly and then ordered. "Who's your friend here?"

The Hokage eyed him and Shin gave him his best innocent smile.

"Hello Hokage-sama, my name is Shin. I met Naruto at the park yesterday."

"Yeah, he's an orphan too and now he's staying with me dattebayo!" Naruto chimed in. Then a stack of ramen bowls arrived and the blonde started inhaling the ramen. Shin stared in disbelief at how fast he was eating. His own bowl arrived and he gingerly sipped at the broth. It had a lot more flavor than the food he was used to.

"Hmm, that's very interesting," the Hokage said, eyeing him warily. "I don't recall any orphans in the village with your name, and why aren't you staying in the orphanage?" The Hokage paused and Shin stilled, trying to remain calm while eating his noodles. Shin didn't answer him and tried to look as focused on the ramen as Naruto was. He couldn't think up an excuse that would pass the Hokage's scrutiny.

The ramen in his bowl disappeared quickly, and Shin lost his excuse to stall. He glanced up and saw the Hokage talking with Naruto about the academy. He noticed that all of them were done with their food. The Hokage stood up to leave.

"Naruto-kun, why don't you go practice the leaf-exercise some more, I'm sure that will help you get your bunshin down. Meanwhile, Shin-kun, follow me to my office so we can talk about your living arrangements."

"You got it jiji, and once I get this down you better be ready to give me your hat dattebayo!" Naruto then ran out of the shop. "See you later Shin-kun!"

The Hokage gestured for him to follow him. He was too careless hanging out with Naruto. He didn't even last one day on his self-imposed infiltration of Konoha.

When they got to his office, the Hokage sat down behind his desk and smiled at Shin, who sat down in front of him. Then the Hokage hardened his gaze.

"So Shin-kun, do you mind telling me why a ROOT agent is playing orphan and staying with Naruto-kun?"

Shin's body stilled and interrogation protocol filled his thoughts. When captured by the enemy, close of your senses. Don't talk about the mission or your comrades. Don't talk at all. His mind started to close down and Shin became only dimly aware of what was happening in the room around him.

The Hokage said some words that Shin didn't hear, and made a few hand gestures. Eventually, a man with long blonde hair entered the room. He sat down in the other chair and Shin heard the Hokage brief him. He recognized the man as Inoichi Yamanaka and he started preparing the mental defenses he was taught.

Then Inoichi clapped loudly in front of his face before his vision was filled with a flash of light. He felt a sharp pain on his neck and he fell unconscious.

The Hokage stared at Inoichi as the man examined Shin's body. He found a few storage seals, but nothing more. Not even the usual silencing seal on the back of the tongue that Danzo always used. The boy must not have even completed his training yet.

"We are going to have to take this carefully to not scare him off Hokage-sama. Even though the boy hasn't finished his training yet, it'd be best if I could avoid using my mind-transfer jutsu on him."

"Yes, I agree," Sarutobi said, and sighed. "The boy seems much too young. I shut down ROOT to stop things like this from happening in the first place. He probably was an orphan here before Danzo took him. If we can get some concrete information from him we'd have the evidence to shut the program down for good."

Inoichi hummed in agreement. "The boy will wake up in a moment. Let's prepare a more calming environment for him."

Shin opened eyes to see a cup of steaming tea on the desk in front of him. The Hokage and Inoichi were smiling at him. Shin straightened up in his chair and eyed them warily. Why wasn't he in an interrogation room?

"Ah, sorry about that Shin-kun," the Hokage said. "You were starting to shut down on us there. You shouldn't even know that technique to resist torture, but anyway it won't be required here. I'd just like to talk with you." Then the man's eyes crinkled with another smile.

Shin remained silent. Maybe they could help him, but he knew he would have to betray ROOT too. While he disagreed with Danzo-sama's methods, the organization was still necessary.

Inoichi spoke up. "Why don't you relax and have some tea Shin-kun. We'd like you to get comfortable, this conversation could take a while."

Shin stared at him and then the tea. It looked good, but they might have drugged it. No, if they wanted to drug him they would have done while he was unconscious. The tea was probably safe. He cautiously grasped the porcelain cup and blew on the liquid before taking a sip. It burned his tongue anyway, but he didn't react. He liked the taste anyway.

"Now, let's get down to business Shin-kun," the Hokage said. "We know that if you were sent to infiltrate Konoha, you would have had a flawless cover and we never would have noticed you. So the question is, why did you leave your base?"

Shin didn't respond right away. He had to make sure his answer for the Hokage was perfect, just like his mission reports.

"I wanted to leave," his voice whispered out.

Inoichi hummed at his response. Shin wondered what kind of insight the man gleamed at his thoughts from it.

"Well that's sounds perfectly fine Shin-kun. So, how did you end up with Naruto-kun?"

Shin saw no reason not to answer the Hokage's questions so far. Nothing he said betrayed his comrades so far.

"I went to the park to figure out what to do next. The Naruto-san wanted to play a game, and I complied to blend in. Then he dragged me to his apartment when he found out I didn't have anywhere to stay."

The Hokage smiled. "Yes, that sounds like Naruto-kun. You probably would have blended in better if you hadn't played with him. He attracts a lot of attention, yes?"

"Hai."

"So are you leaving ROOT for good, or should we send for Danzo to get you?" Inoichi said.

"No!" Shin shouted out, before clamping his jaws shut. He bowed his head. "Sorry for the outburst Hokage-sama, I am ready for my punishment." Shin kept his head bowed. He deserved to be sent to the hole for that.

The room went silent, then he felt a hand on his shoulder. "There's no need that Shin-kun, it's alright." Inoichi said.

"But I need a punishment."

Inoichi hummed again before responding. "Finish your tea then," he said, and handed him his cup. It was still quite hot. Shin instantly drained the liquid, ignoring the burning in his throat.

The room went silent again as the two men stared at him. "Alright then," the Hokage said. "Why did you decide to leave ROOT?"

Shin's thought's spun. How little could he say and still give them enough information?

The door to the office burst open and a young boy with a large scarf trailing behind him ran in.

"Surprise attack!" The kid shouted, and threw two shuriken at the Hokage. Shin sprang from his seat and caught them midair. He was about to attack the boy when Inoichi held him back.

"That won't be necessary Shin-kun, my grandson didn't mean any harm." The Hokage said. Shin looked down at the Shuriken in his hands and saw that they were rubber. Inoichi released his grip and Shin slowly sat back down.

"Now Konohamaru, this is an important meeting. I'm sorry, but you'll have to leave. I'll see you tonight at the compound."

"Fine gramps, but next time I'm gonna get you!" The boy shouted before stomping out and slamming the door behind him.

"Now, where were we Shin-kun?" The old shinobi said.

Shin considered his answer for another moment. "I thought his training methods were wasteful."

The two men tried to get him to elaborate, but that was all that Shin was willing to say. Any more and he thought he would provide some evidence they were fishing for against Danzo-sama.

They finally gave up. "Well then," Inoichi started. "What would you like to do now?"

There wasn't much for him to consider this time. He only had one way to be useful, he just didn't know how to do it.

"I would like to be an official shinobi," he said.

The Hokage smiled at him again. "That can easily be arranged Shin-kun. I have an arrangement that I think you will find acceptable. You will attend the academy for the next six month and then you will be allowed to take the genin exam along with Naruto-kun. Unfortunately, you will not be in the same class because you are two years younger than him, and Iruka's class is already full. I would also like you to see Inoichi once a week to help you adjust to life outside ROOT. Is this agreeable?"

"Hai, Hokage-sama."

"Good, good. The apartment next to Naruto's is free, so I'll arrange it so you can live there. You will also receive the same orphan stipend that he is until you take the exam. And don't worry about being taken back to ROOT, I will talk to Danzo about your new arrangements."

A breath he didn't know he was holding left his chest. He bowed his head again. "Thank you Hokage-sama."

"It's no trouble Shin-kun. Come see me if you have any trouble. Inoichi will help get you settled. I expect great things from you in the future."

Later that evening, Shin heard a knock from the door of his bare apartment. He answered it to find Naruto standing there with a smile on his face.

"Hey Shin-kun! Hokage-jiji told me you are going to be a ninja now too!" He threw his arm around his shoulder and pulled Shin closer. "He also told me to help you get settled in, and that you had some personal problems to deal with. But don't worry about that, us orphans gotta stick together dattebayo!" His smile got wider and he gave him a thumbs up. "Don't worry about anything Shin-kun, you're Onii-san will help you out!"

Shin stared at the blond blankly.

"Hai, Naruto-san."

AN:

Shin is an OC, and not related in any way to Sai's partner. I hope you guy's enjoy, I am writing it to get more experience with longer stories. Sorry if there is any typos, I don't have a beta reader. I'll try to update weekly at least.


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